Tissue samples
Twenty-one pairs of PCa tissue samples and adjacent normal tissues were collected from the Second Affiliated Hospital of Xi'an Jiaotong University between June 2019 and December 2020. This study was approved by the Ethics Committees of the Second Affiliated Hospital of Xi'an Jiaotong University, and was carried out in accordance with the principles of the Declaration of Helsinki. Each participant did not receive radiotherapy and chemotherapy before tissue collection and signed written informed consent before the study. All samples were stored at −80℃ until required for further analysis.
Cell culture
Human PCa cell lines PC-3, LNCaP, DU145 and normal prostate epithelial cell RWPE-1 were purchased from American Type Culture Collection (ATCC; Manassas, VA, USA). All cells were cultured as recommended in DMEM (Gibco, Rockville, MD, USA) containing 1% antibiotics (Gibco) and 10% FBS (Gibco) under 5% CO2 at 37℃. Before using in this study, all cell lines were authenticated by STR profiling and tested for mycoplasma contamination in June 2019.
Cell transfection
The RHPN1-AS1 shRNA (sh-RHPN1-AS1) or negative control shRNA (sh-NC), RHPN1-AS1 overexpression vector (RHPN1-AS1) or pcDNA3.1 empty vector (pcDNA3.1), miR-7-5p mimic or NC mimic, miR-7-5p inhibitor or NC inhibitor, small interfering RNA of Epidermal growth factor receptor (EGFR, si-EGFR) or si-NC were chemically synthesized and provided by Gene Pharma (Shanghai, China). The plasmid, sh-RNA and siRNAs were transfected into LNCaP and PC3 cells for 48 h with Lipofectamine 3000 according to the manufacturer’s instructions, and RT-qPCR checked the transfection efficiency.
RNA isolation of nuclear and cytoplasmic fractions
The RHPN1-AS1 content in the cell cytoplasm and cell nucleus of PC3 cells was assayed following the protocol of PARIS™ Kit (AM1921, Invitrogen). After cells were treated with cell fractionation buffer and then centrifuged, RT-qPCR was applied to determine the expression levels of NNT-AS1 in cytoplasmic and nuclear fractions, with GAPDH (cytoplasmic control) and U6 (nuclear control) as respective controls.
Bioinformatics analysis and dual-luciferase reporter gene assay
The online tool starBase v2.0 (http://starbase.sysu.edu.cn/) was used to predict the potential target genes and analyze the specific binding sites.
The relationship between miR-7-5p and RHPN1-AS1 or EGFR was verified by dual-reporter gene assay. In brief, the pmirGLO vectors (Promega, Madison, WI, USA) containing the sequences of RHPN1-AS1 wild type with the miR-7-5p binding sites or RHPN1-AS1 mutant with the mutated miR-7-5p binding sites, or containing the sequences of wild type EGFR 3′ untranslated region (UTR) with the miR-7-5p binding sites or mutant EGFR 3′ UTR with the mutated miR-7-5p binding sites were obtained from Sangon Biotech and inserted into the pmirGLO vectors (Promega, Madison, WI, USA) for the construction of reporters. The 293T cells were co-transfected with above the pmirGLO vectors and miR-7-5p mimic or NC mimic, respectively. After 48 h later, the luciferase activity was determined with the Dual-Luciferase Reporter Assay Kit (Promega).
RT‑qPCR analysis
Reverse transcription‑quantitative polymerase chain reaction (RT-qPCR) was performed by using ABI PRISM 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) according to the manufacturer’s instructions. Total RNA was isolated from cells and tumors with RNeasy Mini Kit (Qiagen, Valencia, CA). RNA quality was monitored and quantified by using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). The RNA samples were reverse transcribed into cDNA by using a cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA). The cDNA (100 ng per sample) was subjected to qPCR analysis. The RT-qPCR cycling conditions consisted of 95℃ for 3 min; then 35 cycle amplification for 35 s at 95℃, 45 s at 58℃, 30 s at 72℃; followed by 10 min at 72℃. The primers used in this study were synthesized from Sangon Biotech (Shanghai, China). Primers sequences were as follows: RHPN1-AS1 F: 5′-GCT CCT GGT CAT CAA GTT CCT CT-3′, R: 5′-GCA CAG GCA CCA GAA TGA TCC-3′; miR-7-5p F: 5′-TGT TGT TTT GTG AT-3′, R: 5′-GTG CAG GGT CCG AGG T-3′; U6 F: 5′-CAC TGG GTG CGG CAG GT-3′, R: 5′-TCA TCA CCG ATC GAT ACG ATG A-3′; EGFR F: 5′- TGG TCA AGT GCT GGA TGA TAG A-3′, R: 5′- ACG GTA GAA GTT GGA GTC TGT A-3′; GAPDH F: 5’- AAG TTC AAC GGC ACA GTC AAG G-3’, R: 5’- CAT ACT CAG CAC CAG CAT CAC C -3’. Analysis of the relative quantity gene expression was normalized by U6 and GAPDH expression and was performed by using the 2-ΔΔCt method.
Western blot analysis
Cells or tissues were lysed with lysis buffer (150 mM NaCl, 1.0% NP-40 or 0.1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris-HCl (pH 8.0), and protease inhibitors). After incubation on ice for 30 min, the homogenate was centrifuged at 14,000 rpm for 30 min at 4℃, and the protein contents in the supernatant were quantified by BCA methods. Total protein was extracted from the supernatants, separated by 12% SDS-PAGE and transferred to PVDF membranes. The appropriate membranes were blocked by 5% BSA for 1 h at room temperature and incubated with primary antibodies, including anti-EGFR (1:1000), anti-LC3-Ⅰ (1:1000), anti- LC3-Ⅱ (1:1000), anti-cleaved-caspase-3 (1:1000), anti-RARP (1:1000), anti-cleaved-RARP (1:1000), anti-Beclin-1 (1:1000), anti-Atg2 (1:1000), anti-p62 (1:1000), anti-Bax (1:1000), anti-Bcl-2 (1:1000), anti-PI3K (1:1000), anti-p-PI3K (1:1000), anti-AKT (1:1000), anti-p-AKT (1:1000), anti-mTOR (1:1000), anti-p-mTOR (1:1000)and anti-β-actin (1:1000) at 4℃ overnight. Then, ant-Rabbit to mouse polyclonal secondary antibody (1:1000) was incubated for 2 h at room temperature. All immunoblots were visualized by using the ChemiDoc MP System (Bio-Rad protein assay; Bio-Rad, Segrate, Italy) and the enhanced chemiluminescence reagents (Pierce, Rockford, IL, USA). The protein levels were quantitated by Quantity One software (Bio-Rad Laboratories, Hercules, CA).
Immunofluorescence
Cells were grown on glass coverslips to a confluence of 30-50%. Then, they were transfected with sh-RHPN1-AS1 for 6, 24 and 48 h, washed twice with PBS, and fixed for 10 min in 4% paraformaldehyde. Cells were permeabilized in 0.5% Triton X-100, washed, and blocked for 2 h in 5% normal serum. After blocking, the cells were incubated with anti-LC3 (1:500) for 24 h at 4 ℃, washed with PBS and incubated with fluorescently labeled secondary antibody (1:500) and DAPI (5 μg/mL) for 2 h at room temperature. Finally, coverslips were washed and mounted with Vectashield (Solarbio). Immunofluorescence staining was imaged using a fluorescence microscope (Olympus). Five representative fields were captured at × 200 magnification, and the numbers of cells expressing target proteins in the cytoplasm and the nucleus (overlapping with DAPI) cells were counted.
Transmission electron microscopy (ETM)
PC3 cells were harvested after transfection with miR-7-5p mimic or NC mimic, fixed with ice-cold 2.5% glutaraldehyde in PBS for 2 h, post-fixed in 1% osmium tetroxide, dehydrated in a graded series of ethanol (50-100%) and acetone, and embedded in Epon. Representative areas were chosen for ultrathin sectioning and examined with a transmission electron microscope.
Vital staining with acridine orange (AO) or monodansylcadaverine (MDC) staining
PCa cells were seeded in a 24-well culture plate and after subsequent treatments, cells were stained with AO (1 μg/mL) or MDC (0.05 mmol/L) directly for 10 min at 37℃, and then observed under the fluorescence microscope (Olympus, Tokyo, Japan).
Transwell assay
PC3 cells in the logarithmic growth phase were digested and counted, and were cultured in the upper transwell chamber, with 5 × 104 cells/well and 200 µL serum-free medium. Subsequently, 500 µL DMEM containing 10% FBS was added to the lower chamber. After incubation at 37℃ with 5% CO2 for 24 h, the upper chamber cells were carefully removed. And the lower membrane cells were fixed in formaldehyde for 15 min, and then stained with crystal violet (Beyotime, China) for 20 min. Ultimately, 10 fields were randomly selected by using an optical microscope (Olympus, Tokyo, Japan).
Flow Cytometry analysis
PC3 and LNCaP cells after transfection were digested, collected, and re-suspended in Binding Buffer, and then added with 5 μL Annexin V-FITC regent and 10 μL propidium iodide (PI) regent, mixed gently, and placed in the dark at room temperature for 15 min. After washing in PBS, apoptotic cells were analyzed by flow cytometry (BD FACSCalibur cytometer, Becton Dickinson, San Jose, CA, USA) using an Annexin V-FITC apoptosis detection kit (Beyotime Biotechnology, China) following the manufacturer’s instructions.
Cell counting kit-8 (CCK-8) assay
PC3 cell viability was examined by using a Cell Counting Kit-8 (CCK-8, Dojindo, JPN) following the user’s guide. 1 × 103 cells/well after transfection were harvested and seeded into 96-well plates). After that, cells were cultured and processed with 10 μL of CCK-8 solution for 12, 24, 36, 48 or 72 h. Finally, absorbance at 450 nm was examined by using a microplate reader (Olympus, Tokyo, Japan).
Statistical analysis
The values are shown as the means ± SEM for triplicate experiments, and significant differences were calculated using the ANOVA test and Student’s t-test. Levels of statistical significance were set at P<0.05 or 0.01 as indicated.